arq5x

# Download the raw CADD TSV and Tabix index (no annotations, just scores)
wget http://krishna.gs.washington.edu/download/CADD/v1.0/whole_genome_SNVs.tsv.gz
wget http://krishna.gs.washington.edu/download/CADD/v1.0/whole_genome_SNVs.tsv.gz.tbi

# it is big. 79Gb
ls -ltrh whole_genome_SNVs.tsv.gz
-rw-r--r-- 1 arq5x users 79G Sep 26 01:44 whole_genome_SNVs.tsv.gz

# for testing, let's play with the chr22 intervals
tabix whole_genome_SNVs.tsv.gz 22 | bgzip > whole_genome_SNVs.tsv.22.gz

richardcornish

Git notes

Start

1. Install Git
2. Create a GitHub account
3. Open Terminal /Applications/Utilities/Terminal.app

Configure

mick001

# Load the raw training data and replace missing values with NA
training.data.raw <- read.csv('train.csv',header=T,na.strings=c(""))

# Output the number of missing values for each column
sapply(training.data.raw,function(x) sum(is.na(x)))

# Quick check for how many different values for each feature
sapply(training.data.raw, function(x) length(unique(x)))

# A visual way to check for missing data

mick001

# Set a seed
set.seed(500)

library(MASS)
data <- Boston

# Check that no data is missing
apply(data,2,function(x) sum(is.na(x)))

# Train-test random splitting for linear model

mfansler

#!/bin/bash                                                                                                                                    

if [ "$#" -ne 1 ]; then
  echo -e "Incorrect number of parameters! Usage:\n    index-gtf.sh <file.gtf(.gz)>" >&2
  exit 1
fi

gtf="$1"

if [[ $gtf =~ \.gz$ ]]; then

max-mapper

discdiver

If you are on a Mac, substitute command for control. Don't type the + (it means press both keys at once).

Shortcuts when in either command mode (outside the cells) or edit mode (inside a cell):

• Shift + Enter run selected cell or cells - if no cells below, insert a code cell below

• Ctrl + B toggle hide/show left sidebar

• Ctrl + S save and checkpoint

• Ctrl + Shift + S save as

elowy01

*bcftools filter
*Filter variants per region (in this example, print out only variants mapped to chr1 and chr2)
qbcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz

*printing out info for only 2 samples:
bcftools view -s NA20818,NA20819 filename.vcf.gz

*printing stats only for variants passing the filter:
bcftools view -f PASS filename.vcf.gz

m-radzikowski

#!/usr/bin/env bash

set -Eeuo pipefail
trap cleanup SIGINT SIGTERM ERR EXIT

script_dir=$(cd "$(dirname "${BASH_SOURCE[0]}")" &>/dev/null && pwd -P)

usage() {
  cat <<EOF
Usage: $(basename "${BASH_SOURCE[0]}") [-h] [-v] [-f] -p param_value arg1 [arg2...]

jimbojsb

Step 0:

Get Homebrew installed on your mac if you don't already have it

Step 1:

Install highlight. "brew install highlight". (This brings down Lua and Boost as well)

Step 2: